Yang-Yu Liu (Y-Y Liu, Yangyu Liu)

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 78

Top Venues

Nature communications

Proceedings of the National Academy of Sciences of the United States of America

bioRxiv : the preprint server for biology

Bioinformatics (Oxford, England)

Harvard Medical School

University of Illinois at Urbana-Champaign (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Harvard Medical School Jul 01 2014

United States

Assistant Professor :: Medicine

Brigham and Women's Hospital Jul 01 2013

United States

Associate Scientisit :: Medicine

Harvard Medical School Jul 01 2013 - Jul 01 2014

United States

Lecturer :: Medicine

Northeastern University Oct 01 2012 - May 31 2013

United States

Research Assistant Professor :: Physics

Northeastern University Jun 01 2009 - Oct 01 2012

United States

Postdoctoral Research Associate :: Physics

Education History

University of Illinois at Urbana-Champaign Aug 17 2003 - May 20 2009

United States

PHD :: Physics

Publications

Chengyi Long, Jie Deng, Jen Nguyen, Yang-Yu Liu, Eric J Alm, Ricard Solé, Serguei Saavedra
Structured community transitions explain the switching capacity of microbial systems. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Yao Meng, Sean P Cornelius, Yang-Yu Liu, Aming Li
Dynamics of collective cooperation under personalised strategy updates. Nature communications 15 (1) (2024)
Chengyi Long, Jie Deng, Jen Nguyen, Yang-Yu Liu, Eric J Alm, Ricard Solé, Serguei Saavedra
Structured community transitions explain the switching capacity of microbial systems. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Chengyi Long, Jie Deng, Jen Nguyen, Yang-Yu Liu, Eric J Alm, Ricard Solé, Serguei Saavedra
Structured community transitions explain the switching capacity of microbial systems. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Yandong Xiao, Xiaokang Lei, Zhicheng Zheng, Yalun Xiang, Yang-Yu Liu, Xingguang Peng
Perception of motion salience shapes the emergence of collective motions. Nature communications 15 (1) (2024)
Yao Meng, Sean P Cornelius, Yang-Yu Liu, Aming Li
Dynamics of collective cooperation under personalised strategy updates. Nature communications 15 (1) (2024)
Lu Wu, Xu-Wen Wang, Zining Tao, Tong Wang, Wenlong Zuo, Yu Zeng, Yang-Yu Liu, Lei Dai
Data-driven prediction of colonization outcomes for complex microbial communities. Nature communications 15 (1) (2024)
Yao Meng, Sean P Cornelius, Yang-Yu Liu, Aming Li
Dynamics of collective cooperation under personalised strategy updates. Nature communications 15 (1) (2024)
Lu Wu, Xu-Wen Wang, Zining Tao, Tong Wang, Wenlong Zuo, Yu Zeng, Yang-Yu Liu, Lei Dai
Data-driven prediction of colonization outcomes for complex microbial communities. Nature communications 15 (1) (2024)
Lu Wu, Xu-Wen Wang, Zining Tao, Tong Wang, Wenlong Zuo, Yu Zeng, Yang-Yu Liu, Lei Dai
Data-driven prediction of colonization outcomes for complex microbial communities. Nature communications 15 (1) (2024)
Chengyi Long, Jie Deng, Jen Nguyen, Yang-Yu Liu, Eric J Alm, Ricard Solé, Serguei Saavedra
Structured community transitions explain the switching capacity of microbial systems. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Anne-Josée Guimond, Shanlin Ke, Shelley T Tworoger, Tianyi Huang, Andrew T Chan, Laura D Kubzansky, Yang-Yu Liu
Fulfilled Mind, Healthy Gut? Relationships of Eudaimonic Psychological Well-Being With the Gut Microbiome in Postmenopausal Women. Psychosomatic medicine 86 (5) (2024)
Chengyi Long, Jie Deng, Jen Nguyen, Yang-Yu Liu, Eric J Alm, Ricard Solé, Serguei Saavedra
Structured community transitions explain the switching capacity of microbial systems. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Anne-Josée Guimond, Shanlin Ke, Shelley T Tworoger, Tianyi Huang, Andrew T Chan, Laura D Kubzansky, Yang-Yu Liu
Fulfilled Mind, Healthy Gut? Relationships of Eudaimonic Psychological Well-Being With the Gut Microbiome in Postmenopausal Women. Psychosomatic medicine 86 (5) (2024)
Yandong Xiao, Xiaokang Lei, Zhicheng Zheng, Yalun Xiang, Yang-Yu Liu, Xingguang Peng
Perception of motion salience shapes the emergence of collective motions. Nature communications 15 (1) (2024)
Yandong Xiao, Xiaokang Lei, Zhicheng Zheng, Yalun Xiang, Yang-Yu Liu, Xingguang Peng
Perception of motion salience shapes the emergence of collective motions. Nature communications 15 (1) (2024)
Shanlin Ke, Javier A Villafuerte Gálvez, Zheng Sun, Yangchun Cao, Nira R Pollock, Xinhua Chen, Ciarán P Kelly, Yang-Yu Liu
Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection. bioRxiv : the preprint server for biology (2024)
Chengyi Long, Jie Deng, Jen Nguyen, Yang-Yu Liu, Eric J Alm, Ricard Solé, Serguei Saavedra
Structured community transitions explain the switching capacity of microbial systems. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Yao Meng, Sean P Cornelius, Yang-Yu Liu, Aming Li
Dynamics of collective cooperation under personalised strategy updates. Nature communications 15 (1) (2024)
Chengyi Long, Jie Deng, Jen Nguyen, Yang-Yu Liu, Eric J Alm, Ricard Solé, Serguei Saavedra
Structured community transitions explain the switching capacity of microbial systems. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Shanlin Ke, Javier A Villafuerte Gálvez, Zheng Sun, Yangchun Cao, Nira R Pollock, Xinhua Chen, Ciarán P Kelly, Yang-Yu Liu
Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection. bioRxiv : the preprint server for biology (2024)
Lu Wu, Xu-Wen Wang, Zining Tao, Tong Wang, Wenlong Zuo, Yu Zeng, Yang-Yu Liu, Lei Dai
Data-driven prediction of colonization outcomes for complex microbial communities. Nature communications 15 (1) (2024)
Chengyi Long, Jie Deng, Jen Nguyen, Yang-Yu Liu, Eric J Alm, Ricard Solé, Serguei Saavedra
Structured community transitions explain the switching capacity of microbial systems. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Anne-Josée Guimond, Shanlin Ke, Shelley T Tworoger, Tianyi Huang, Andrew T Chan, Laura D Kubzansky, Yang-Yu Liu
Fulfilled Mind, Healthy Gut? Relationships of Eudaimonic Psychological Well-Being With the Gut Microbiome in Postmenopausal Women. Psychosomatic medicine 86 (5) (2024)
Lu Wu, Xu-Wen Wang, Zining Tao, Tong Wang, Wenlong Zuo, Yu Zeng, Yang-Yu Liu, Lei Dai
Data-driven prediction of colonization outcomes for complex microbial communities. Nature communications 15 (1) (2024)
Can Chen, Scott T Weiss, Yang-Yu Liu
Graph convolutional network-based feature selection for high-dimensional and low-sample size data. Bioinformatics (Oxford, England) 39 (4) (2023)
Xu-Wen Wang, Lorenzo Madeddu, Kerstin Spirohn, Leonardo Martini, Adriano Fazzone, Luca Becchetti, Thomas P Wytock, István A Kovács, Olivér M Balogh, Bettina Benczik, Mátyás Pétervári, Bence Agg, Péter Ferdinandy, Loan Vulliard, J Formula See Text Rg Menche, Stefania Colonnese, Manuela Petti, Gaetano Scarano, Francesca Cuomo, Tong Hao, Florent Laval, Luc Willems, Jean-Claude Twizere, Marc Vidal, Michael A Calderwood, Enrico Petrillo, Albert-László Barabási, Edwin K Silverman, Joseph Loscalzo, Paola Velardi, Yang-Yu Liu
Assessment of community efforts to advance network-based prediction of protein-protein interactions. Nature communications 14 (1) (2023)
Xu-Wen Wang, Lu Wu, Lei Dai, Xiaole Yin, Tong Zhang, Scott T Weiss, Yang-Yu Liu
Ecological dynamics imposes fundamental challenges in community-based microbial source tracking. iMeta 2 (1) (2023)
Changjun Fan, Mutian Shen, Zohar Nussinov, Zhong Liu, Yizhou Sun, Yang-Yu Liu
Reply to: Deep reinforced learning heuristic tested on spin-glass ground states: The larger picture. Nature communications 14 (1) (2023)
Xu-Wen Wang, Zheng Sun, Huijue Jia, Sebastian Michel-Mata, Marco Tulio Angulo, Lei Dai, Xuesong He, Scott T Weiss, Yang-Yu Liu
Identifying keystone species in microbial communities using deep learning. bioRxiv : the preprint server for biology (2023)
Can Chen, Scott T Weiss, Yang-Yu Liu
Graph convolutional network-based feature selection for high-dimensional and low-sample size data. Bioinformatics (Oxford, England) 39 (4) (2023)
Xu-Wen Wang, Lu Wu, Lei Dai, Xiaole Yin, Tong Zhang, Scott T Weiss, Yang-Yu Liu
Ecological dynamics imposes fundamental challenges in community-based microbial source tracking. iMeta 2 (1) (2023)
Andrea Aparicio, Diane R Gold, Scott T Weiss, Augusto A Litonjua, Kathleen Lee-Sarwar, Yang-Yu Liu
Association of vitamin D level and maternal gut microbiome during pregnancy: Findings from a randomized controlled trial of antenatal vitamin D supplementation. medRxiv : the preprint server for health sciences (2023)
Leyuan Li, Tong Wang, Zhibin Ning, Xu Zhang, James Butcher, Joeselle M Serrana, Caitlin M A Simopoulos, Janice Mayne, Alain Stintzi, David R Mack, Yang-Yu Liu, Daniel Figeys
Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics. Nature communications 14 (1) (2023)
Changjun Fan, Mutian Shen, Zohar Nussinov, Zhong Liu, Yizhou Sun, Yang-Yu Liu
Searching for spin glass ground states through deep reinforcement learning. Nature communications 14 (1) (2023)
Can Chen, Scott T Weiss, Yang-Yu Liu
Graph convolutional network-based feature selection for high-dimensional and low-sample size data. Bioinformatics (Oxford, England) 39 (4) (2023)
Xu-Wen Wang, Zheng Sun, Huijue Jia, Sebastian Michel-Mata, Marco Tulio Angulo, Lei Dai, Xuesong He, Scott T Weiss, Yang-Yu Liu
Identifying keystone species in microbial communities using deep learning. Nature ecology & evolution (2023)
Xu-Wen Wang, Lorenzo Madeddu, Kerstin Spirohn, Leonardo Martini, Adriano Fazzone, Luca Becchetti, Thomas P Wytock, István A Kovács, Olivér M Balogh, Bettina Benczik, Mátyás Pétervári, Bence Agg, Péter Ferdinandy, Loan Vulliard, J Formula See Text Rg Menche, Stefania Colonnese, Manuela Petti, Gaetano Scarano, Francesca Cuomo, Tong Hao, Florent Laval, Luc Willems, Jean-Claude Twizere, Marc Vidal, Michael A Calderwood, Enrico Petrillo, Albert-László Barabási, Edwin K Silverman, Joseph Loscalzo, Paola Velardi, Yang-Yu Liu
Assessment of community efforts to advance network-based prediction of protein-protein interactions. Nature communications 14 (1) (2023)
Xu-Wen Wang, Lorenzo Madeddu, Kerstin Spirohn, Leonardo Martini, Adriano Fazzone, Luca Becchetti, Thomas P Wytock, István A Kovács, Olivér M Balogh, Bettina Benczik, Mátyás Pétervári, Bence Agg, Péter Ferdinandy, Loan Vulliard, J Formula See Text Rg Menche, Stefania Colonnese, Manuela Petti, Gaetano Scarano, Francesca Cuomo, Tong Hao, Florent Laval, Luc Willems, Jean-Claude Twizere, Marc Vidal, Michael A Calderwood, Enrico Petrillo, Albert-László Barabási, Edwin K Silverman, Joseph Loscalzo, Paola Velardi, Yang-Yu Liu
Assessment of community efforts to advance network-based prediction of protein-protein interactions. Nature communications 14 (1) (2023)
Andrea Aparicio, Zheng Sun, Diane R Gold, Augusto A Litonjua, Scott T Weiss, Kathleen Lee-Sarwar, Yang-Yu Liu
Genotype-microbiome-metabolome associations in early childhood, and their link to BMI and childhood obesity. medRxiv : the preprint server for health sciences (2023)
Lu Wu, Xu-Wen Wang, Zining Tao, Tong Wang, Wenlong Zuo, Yu Zeng, Yang-Yu Liu, Lei Dai
Data-driven prediction of colonization outcomes for complex microbial communities. bioRxiv : the preprint server for biology (2023)
Tong Wang, Yuanqing Fu, Menglei Shuai, Ju-Sheng Zheng, Lu Zhu, Qi Sun, Frank B Hu, Scott T Weiss, Yang-Yu Liu
Microbiome-based correction of nutrient profiles derived from self-reported dietary assessments. bioRxiv : the preprint server for biology (2023)
Can Chen, Scott T Weiss, Yang-Yu Liu
Graph convolutional network-based feature selection for high-dimensional and low-sample size data. Bioinformatics (Oxford, England) 39 (4) (2023)
Tong Wang, Hannah D Holscher, Sergei Maslov, Frank B Hu, Scott T Weiss, Yang-Yu Liu
Predicting metabolic response to dietary intervention using deep learning. bioRxiv : the preprint server for biology (2023)
Changjun Fan, Mutian Shen, Zohar Nussinov, Zhong Liu, Yizhou Sun, Yang-Yu Liu
Searching for spin glass ground states through deep reinforcement learning. Nature communications 14 (1) (2023)
Xu-Wen Wang, Lu Wu, Lei Dai, Xiaole Yin, Tong Zhang, Scott T Weiss, Yang-Yu Liu
Ecological dynamics imposes fundamental challenges in community-based microbial source tracking. iMeta 2 (1) (2023)
Changjun Fan, Mutian Shen, Zohar Nussinov, Zhong Liu, Yizhou Sun, Yang-Yu Liu
Searching for spin glass ground states through deep reinforcement learning. Nature communications 14 (1) (2023)
Changjun Fan, Mutian Shen, Zohar Nussinov, Zhong Liu, Yizhou Sun, Yang-Yu Liu
Searching for spin glass ground states through deep reinforcement learning. Nature communications 14 (1) (2023)
Xu-Wen Wang, Lu Wu, Lei Dai, Xiaole Yin, Tong Zhang, Scott T Weiss, Yang-Yu Liu
Ecological dynamics imposes fundamental challenges in community-based microbial source tracking. iMeta 2 (1) (2023)
Xu-Wen Wang, Yang Hu, Giulia Menichetti, Francine Grodstein, Shilpa N Bhupathiraju, Frank B Hu, Xuehong Zhang, Frank B Hu, Scott T Weiss, Yang-Yu Liu
Nutritional redundancy in the human diet and its application in phenotype association studies. Nature communications 14 (1) (2023)
Can Chen, Scott T Weiss, Yang-Yu Liu
Graph convolutional network-based feature selection for high-dimensional and low-sample size data. Bioinformatics (Oxford, England) 39 (4) (2023)
Zheng Sun, Jiang Liu, Meng Zhang, Tong Wang, Shi Huang, Scott T Weiss, Yang-Yu Liu
Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites. Nature communications 14 (1) (2023)
Andrea Aparicio, Diane R Gold, Scott T Weiss, Augusto A Litonjua, Kathleen A Lee-Sarwar, Yang-Yu Liu
Association of Vitamin D Level and Maternal Gut Microbiome during Pregnancy: Findings from a Randomized Controlled Trial of Antenatal Vitamin D Supplementation. Nutrients 15 (9) (2023)
Shanlin Ke, Anne-Josée Guimond, Shelley T Tworoger, Tianyi Huang, Andrew T Chan, Yang-Yu Liu, Laura D Kubzansky
Gut feelings: associations of emotions and emotion regulation with the gut microbiome in women. Psychological medicine (2023)
Can Chen, Chen Liao, Yang-Yu Liu
Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning. Nature communications 14 (1) (2023)
Can Chen, Chen Liao, Yang-Yu Liu
Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning. Nature communications 14 (1) (2023)
Andrea Aparicio, Jorge X Velasco-Hernández, Claude H Moog, Yang-Yu Liu, Marco Tulio Angulo
Structure-based identification of sensor species for anticipating critical transitions. Proceedings of the National Academy of Sciences of the United States of America 118 (51) (2022)
Hongbin Liu, Chen Liao, Lu Wu, Jinhui Tang, Junyu Chen, Chaobi Lei, Linggang Zheng, Chenhong Zhang, Yang-Yu Liu, Joao B Xavier, Lei Dai
Ecological dynamics of the gut microbiome in response to dietary fiber. The ISME journal 16 (8) (2022)
Xu-Wen Wang, Dandi Qiao, Michael H Cho, Dawn L DeMeo, Edwin K Silverman, Yang-Yu Liu
A statistical physics approach for disease module detection. Genome research 32 (10) (2022)
Shanlin Ke, Scott T Weiss, Yang-Yu Liu
Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes. Nature communications 13 (1) (2022)
Zheng Sun, Shi Huang, Meng Zhang, Qiyun Zhu, Niina Haiminen, Anna Paola Carrieri, Yoshiki Vázquez-Baeza, Laxmi Parida, Ho-Cheol Kim, Rob Knight, Yang-Yu Liu
Challenges in benchmarking metagenomic profilers. Nature methods 18 (6) (2021)
Yu Deng, Yue Huang, You Che, Yu Yang, Xiaole Yin, Aixin Yan, Lei Dai, Yang-Yu Liu, Martin Polz, Tong Zhang
Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants. The ISME journal 15 (10) (2021)
Shanlin Ke, Sarah J Mitchell, Michael R MacArthur, Alice E Kane, David A Sinclair, Emily M Venable, Katia S Chadaideh, Rachel N Carmody, Francine Grodstein, James R Mitchell, Yang-Yu Liu
Gut Microbiota Predicts Healthy Late-Life Aging in Male Mice. Nutrients 13 (9) (2021)
Aming Li, Lei Zhou, Qi Su, Sean P Cornelius, Yang-Yu Liu, Long Wang, Simon Asher Levin
Evolution of cooperation on temporal networks. Nature communications 11 (1) (2020)
Jean Celestin Charles Vila, Yang-Yu Liu, Alvaro Sánchez
Dissimilarity-Overlap analysis of replicate enrichment communities. The ISME journal 14 (10) (2020)
Liang Tian, Xu-Wen Wang, Ang-Kun Wu, Yuhang Fan, Jonathan Friedman, Amber Dahlin, Matthew Kaden Waldor, George M Weinstock, Scott T Weiss, Yang-Yu Liu
Deciphering functional redundancy in the human microbiome. Nature communications 11 (1) (2020)
Yandong Xiao, Marco Tulio Angulo, Songyang Lao, Scott T Weiss, Yang-Yu Liu
An ecological framework to understand the efficacy of fecal microbiota transplantation. Nature communications 11 (1) (2020)
Orr Levy, Guy Amit, Dana Vaknin, Tom Snir, Sol Efroni, Peter Castaldi, Yang-Yu Liu, Haim Y Cohen, Amir Bashan
Age-related loss of gene-to-gene transcriptional coordination among single cells. Nature metabolism 2 (11) (2020)
Yize Chen, Marco Tulio Angulo, Yang-Yu Liu
Revealing Complex Ecological Dynamics via Symbolic Regression. BioEssays : news and reviews in molecular, cellular and developmental biology 41 (12) (2019)
Mincheng Wu, Shibo He, Yongtao Zhang, Jiming Chen, Youxian Sun, Yang-Yu Liu, Junshan Zhang, Harold Vincent Poor
A tensor-based framework for studying eigenvector multicentrality in multilayer networks. Proceedings of the National Academy of Sciences of the United States of America 116 (31) (2019)
Marco Tulio Angulo, Claude H Moog, Yang-Yu Liu
A theoretical framework for controlling complex microbial communities. Nature communications 10 (1) (2019)
Abhijeet R Sonawane, Liang Tian, Chin-Yi Chu, Xing Qui, Lu Wang, Jeanne Holden-Wiltse, Alex Grier, Steven R Gill, Mary T Caserta, Ann R Falsey, David J Topham, Edward E Walsh, Thomas J Mariani, Scott T Weiss, Edwin K Silverman, Kimberly Glass, Yang-Yu Liu
Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection. Scientific reports 9 (1) (2019)
Aming Li, S P Cornelius, Yang-Yu Liu, Long Wang, Albert-László Barabási
The fundamental advantages of temporal networks. Science (New York, N.Y.) 358 (6366) (2018)
Gang Yan, Neo D Martinez, Yang-Yu Liu
Degree heterogeneity and stability of ecological networks. Journal of the Royal Society, Interface 14 (131) (2018)
Amitabh Sharma, Arda Halu, Julius L Decano, Megha Padi, Yang-Yu Liu, Rashmi B Prasad, Joao Fadista, Marc Santolini, J Formula See Text Rg Menche, Scott T Weiss, Marc Vidal, Edwin K Silverman, Masanori Aikawa, Albert-László Barabási, Leif C Groop, Joseph Loscalzo
Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes. NPJ systems biology and applications 4 (2018)
Yandong Xiao, Marco Tulio Angulo, Jonathan Friedman, Matthew K Waldor, Scott T Weiss, Yang-Yu Liu
Mapping the ecological networks of microbial communities. Nature communications 8 (1) (2017)
Marco Tulio Angulo, Jaime A Moreno, Gabor Lippner, Albert-László Barabási, Yang-Yu Liu
Fundamental limitations of network reconstruction from temporal data. Journal of the Royal Society, Interface 14 (127) (2017)
Liang Tian, Amir Bashan, Da-Ning Shi, Yang-Yu Liu
Articulation points in complex networks. Nature communications 8 (2017)

Yang-Yu Liu.css-eqlu8i{font-size:small;padding-left:4px;} (Y-Y Liu, Yangyu Liu)

Publication Activity (10 Years)

Top Topics

Top Venues

Yang-Yu Liu (Y-Y Liu, Yangyu Liu)